partis-bcr 1.0.11.post1.dev1__cp312-cp312-manylinux1_x86_64.whl → 1.0.11.post1.dev3__cp312-cp312-manylinux1_x86_64.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (652) hide show
  1. bin/partis +1 -1
  2. bin/partis-test.py +6 -0
  3. bin/partis.py +1 -1
  4. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/partis-test.py +6 -0
  5. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/METADATA +1 -1
  6. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/RECORD +652 -125
  7. python/recombinator.py +2 -0
  8. python/treegenerator.py +1 -1
  9. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  10. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +8 -0
  11. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  12. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  13. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  14. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  15. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  16. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  17. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  18. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  19. test/new-results/annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +8 -0
  20. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  21. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  22. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  23. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  24. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  25. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  26. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  27. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  28. test/new-results/annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  29. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +7 -0
  30. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +7 -0
  31. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +5 -0
  32. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +6 -0
  33. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +7 -0
  34. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  35. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  36. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  37. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +7 -0
  38. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  39. test/new-results/annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  40. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  41. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  42. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  43. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  44. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  45. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  46. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  47. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  48. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  49. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  50. test/new-results/annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  51. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  52. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  53. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  54. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  55. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  56. test/new-results/annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  57. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  58. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  59. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  60. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  61. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  62. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  63. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  64. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  65. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  66. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  67. test/new-results/annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  68. test/new-results/annotate-new-simu.yaml +1 -0
  69. test/new-results/cache-new-partition.csv +59 -0
  70. test/new-results/get-selection-metrics-new-simu.yaml +1 -0
  71. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  72. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  73. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  74. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  75. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  76. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  77. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  78. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  79. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  80. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  81. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  82. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  83. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  84. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  85. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  86. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  87. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  88. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  89. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  90. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  91. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  92. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  93. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  94. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  95. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  96. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  97. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  98. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  99. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  100. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  101. test/new-results/multi-annotate-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  102. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  103. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  104. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  105. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  106. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  107. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  108. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  109. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  110. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  111. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  112. test/new-results/multi-annotate-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  113. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  114. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  115. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  116. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  117. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  118. test/new-results/multi-annotate-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  119. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  120. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  121. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  122. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  123. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  124. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  125. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  126. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  127. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
  128. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_hamming_to_true_naive.csv +4 -0
  129. test/new-results/multi-annotate-new-simu-annotation-performance/sw/mutation/v_muted_bases.csv +4 -0
  130. test/new-results/multi-annotate-new-simu.yaml +1 -0
  131. test/new-results/partition-new-simu/fasttree/iclust-0/fasttree.out +1 -0
  132. test/new-results/partition-new-simu/fasttree/iclust-0/input-seqs.fa +24 -0
  133. test/new-results/partition-new-simu/fasttree/iclust-0/log +23 -0
  134. test/new-results/partition-new-simu/fasttree/iclust-1/fasttree.out +1 -0
  135. test/new-results/partition-new-simu/fasttree/iclust-1/input-seqs.fa +16 -0
  136. test/new-results/partition-new-simu/fasttree/iclust-1/log +23 -0
  137. test/new-results/partition-new-simu/fasttree/iclust-2/fasttree.out +1 -0
  138. test/new-results/partition-new-simu/fasttree/iclust-2/input-seqs.fa +16 -0
  139. test/new-results/partition-new-simu/fasttree/iclust-2/log +22 -0
  140. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_3p_del.csv +7 -0
  141. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/d_5p_del.csv +6 -0
  142. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/dj_insertion.csv +8 -0
  143. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/fv_insertion.csv +10 -0
  144. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_3p_del.csv +4 -0
  145. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/j_5p_del.csv +8 -0
  146. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/jf_insertion.csv +4 -0
  147. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/shm_indel_length.csv +8 -0
  148. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_3p_del.csv +4 -0
  149. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/v_5p_del.csv +4 -0
  150. test/new-results/partition-new-simu-annotation-performance/hmm/boundaries/vd_insertion.csv +6 -0
  151. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  152. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  153. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/d_gene.csv +5 -0
  154. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  155. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  156. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/j_gene.csv +5 -0
  157. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_allele_fraction_correct_vs_per_gene_support.csv +28 -0
  158. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  159. test/new-results/partition-new-simu-annotation-performance/hmm/gene-call/v_gene.csv +5 -0
  160. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_hamming_to_true_naive.csv +5 -0
  161. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/cdr3_muted_bases.csv +5 -0
  162. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_hamming_to_true_naive.csv +4 -0
  163. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/d_muted_bases.csv +4 -0
  164. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/hamming_to_true_naive.csv +5 -0
  165. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_hamming_to_true_naive.csv +4 -0
  166. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/j_muted_bases.csv +5 -0
  167. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/mute_freqs.csv +28 -0
  168. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/muted_bases.csv +5 -0
  169. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_hamming_to_true_naive.csv +4 -0
  170. test/new-results/partition-new-simu-annotation-performance/hmm/mutation/v_muted_bases.csv +4 -0
  171. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_3p_del.csv +8 -0
  172. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/d_5p_del.csv +6 -0
  173. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/dj_insertion.csv +7 -0
  174. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/fv_insertion.csv +4 -0
  175. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_3p_del.csv +4 -0
  176. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/j_5p_del.csv +9 -0
  177. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/jf_insertion.csv +4 -0
  178. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/shm_indel_length.csv +8 -0
  179. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_3p_del.csv +4 -0
  180. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/v_5p_del.csv +4 -0
  181. test/new-results/partition-new-simu-annotation-performance/sw/boundaries/vd_insertion.csv +6 -0
  182. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_fraction_correct_vs_mute_freq.csv +28 -0
  183. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/d_gene.csv +5 -0
  184. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_fraction_correct_vs_mute_freq.csv +28 -0
  185. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/j_gene.csv +5 -0
  186. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_fraction_correct_vs_mute_freq.csv +28 -0
  187. test/new-results/partition-new-simu-annotation-performance/sw/gene-call/v_gene.csv +5 -0
  188. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_hamming_to_true_naive.csv +6 -0
  189. test/new-results/partition-new-simu-annotation-performance/sw/mutation/cdr3_muted_bases.csv +7 -0
  190. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_hamming_to_true_naive.csv +5 -0
  191. test/new-results/partition-new-simu-annotation-performance/sw/mutation/d_muted_bases.csv +5 -0
  192. test/new-results/partition-new-simu-annotation-performance/sw/mutation/hamming_to_true_naive.csv +6 -0
  193. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_hamming_to_true_naive.csv +4 -0
  194. test/new-results/partition-new-simu-annotation-performance/sw/mutation/j_muted_bases.csv +6 -0
  195. test/new-results/partition-new-simu-annotation-performance/sw/mutation/mute_freqs.csv +28 -0
  196. test/new-results/partition-new-simu-annotation-performance/sw/mutation/muted_bases.csv +7 -0
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  634. test/paired/new-results/test/simu/igh+igl/igl.yaml +1 -0
  635. test/paired/new-results/test/simu/igh.yaml +1 -0
  636. test/paired/new-results/test/simu/igk.yaml +1 -0
  637. test/paired/new-results/test/simu/igl.yaml +1 -0
  638. test/paired/new-results/test/simu/meta.yaml +1 -0
  639. test/paired/new-results/test.log +227 -33
  640. test/test.py +6 -0
  641. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-alleles.py +0 -0
  642. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/cf-germlines.py +0 -0
  643. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/compare-plotdirs.py +0 -0
  644. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/extract-pairing-info.py +0 -0
  645. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/gctree-run.py +0 -0
  646. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/get-naive-probabilities.py +0 -0
  647. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/parse-output.py +0 -0
  648. {partis_bcr-1.0.11.post1.dev1.data → partis_bcr-1.0.11.post1.dev3.data}/scripts/split-loci.py +0 -0
  649. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/WHEEL +0 -0
  650. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/entry_points.txt +0 -0
  651. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/licenses/COPYING +0 -0
  652. {partis_bcr-1.0.11.post1.dev1.dist-info → partis_bcr-1.0.11.post1.dev3.dist-info}/top_level.txt +0 -0
test/new-results/test/parameters/data/hmm/hmms/IGHD6-13_star_01.yaml ADDED
@@ -0,0 +1,533 @@
1
+ !!python/object:python.hmmwriter.HMM
2
+ extras:
3
+ gene_prob: 0.21739130434782608
4
+ overall_mute_freq: 0.08760869565217394
5
+ per_gene_mute_freq: 0.12622187310705474
6
+ name: IGHD6-13_star_01
7
+ states:
8
+ - !!python/object:python.hmmwriter.State
9
+ emissions: null
10
+ extras: {}
11
+ name: init
12
+ transitions:
13
+ IGHD6-13_star_01_0: 0.0037593984962406013
14
+ IGHD6-13_star_01_1: 0.0037593984962406013
15
+ IGHD6-13_star_01_10: 0.003341687552213868
16
+ IGHD6-13_star_01_11: 0.0029239766081871343
17
+ IGHD6-13_star_01_12: 0.0025062656641604004
18
+ IGHD6-13_star_01_13: 0.0020885547201336665
19
+ IGHD6-13_star_01_14: 0.001670843776106933
20
+ IGHD6-13_star_01_15: 0.0012531328320801996
21
+ IGHD6-13_star_01_16: 0.0008354218880534663
22
+ IGHD6-13_star_01_17: 0.0004177109440267328
23
+ IGHD6-13_star_01_18: 0.0037593984962406013
24
+ IGHD6-13_star_01_19: 0.0037593984962406013
25
+ IGHD6-13_star_01_2: 0.0037593984962406013
26
+ IGHD6-13_star_01_20: 0.0037593984962406013
27
+ IGHD6-13_star_01_3: 0.007518796992481203
28
+ IGHD6-13_star_01_4: 0.007518796992481203
29
+ IGHD6-13_star_01_5: 0.0037593984962406013
30
+ IGHD6-13_star_01_6: 0.0037593984962406013
31
+ IGHD6-13_star_01_7: 0.0037593984962406013
32
+ IGHD6-13_star_01_8: 0.0037593984962406013
33
+ IGHD6-13_star_01_9: 0.0037593984962406013
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+ insert_left_A: 0.17454350161117077
35
+ insert_left_C: 0.3141783029001074
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+ insert_left_G: 0.21643394199785176
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+ insert_left_T: 0.2234156820622986
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+ - !!python/object:python.hmmwriter.State
39
+ emissions:
40
+ probs:
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+ A: 0.8737781268929452
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+ C: 0.04207395770235158
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+ G: 0.04207395770235158
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+ T: 0.04207395770235158
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+ track: nukes
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+ extras:
47
+ ambiguous_char: N
48
+ ambiguous_emission_prob: 0.25
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+ germline: A
50
+ name: insert_left_A
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+ transitions:
52
+ IGHD6-13_star_01_0: 0.009738001391143055
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+ IGHD6-13_star_01_1: 0.009738001391143055
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+ IGHD6-13_star_01_10: 0.008656001236571604
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+ IGHD6-13_star_01_11: 0.0075740010820001535
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+ IGHD6-13_star_01_12: 0.006492000927428702
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+ IGHD6-13_star_01_13: 0.005410000772857251
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+ IGHD6-13_star_01_14: 0.0043280006182858
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+ IGHD6-13_star_01_15: 0.0032460004637143497
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+ IGHD6-13_star_01_16: 0.0021640003091428993
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+ IGHD6-13_star_01_17: 0.001082000154571449
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+ IGHD6-13_star_01_18: 0.009738001391143055
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+ IGHD6-13_star_01_19: 0.009738001391143055
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+ IGHD6-13_star_01_2: 0.009738001391143055
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+ IGHD6-13_star_01_20: 0.009738001391143055
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+ IGHD6-13_star_01_3: 0.01947600278228611
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+ IGHD6-13_star_01_4: 0.01947600278228611
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+ IGHD6-13_star_01_5: 0.009738001391143055
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+ IGHD6-13_star_01_6: 0.009738001391143055
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+ IGHD6-13_star_01_7: 0.009738001391143055
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+ IGHD6-13_star_01_8: 0.009738001391143055
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+ IGHD6-13_star_01_9: 0.009738001391143055
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+ insert_left_A: 0.15319134841509058
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+ insert_left_C: 0.2757444271471631
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+ insert_left_G: 0.18995727203471233
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+ insert_left_T: 0.19608492597131594
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+ - !!python/object:python.hmmwriter.State
78
+ emissions:
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+ probs:
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+ A: 0.04207395770235158
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+ C: 0.8737781268929452
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+ G: 0.04207395770235158
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+ T: 0.04207395770235158
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
87
+ ambiguous_emission_prob: 0.25
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+ germline: C
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+ name: insert_left_C
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+ transitions:
91
+ IGHD6-13_star_01_0: 0.009738001391143055
92
+ IGHD6-13_star_01_1: 0.009738001391143055
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+ IGHD6-13_star_01_10: 0.008656001236571604
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+ IGHD6-13_star_01_11: 0.0075740010820001535
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+ IGHD6-13_star_01_12: 0.006492000927428702
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+ IGHD6-13_star_01_13: 0.005410000772857251
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+ IGHD6-13_star_01_14: 0.0043280006182858
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+ IGHD6-13_star_01_15: 0.0032460004637143497
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+ IGHD6-13_star_01_16: 0.0021640003091428993
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+ IGHD6-13_star_01_17: 0.001082000154571449
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+ IGHD6-13_star_01_18: 0.009738001391143055
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+ IGHD6-13_star_01_19: 0.009738001391143055
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+ IGHD6-13_star_01_2: 0.009738001391143055
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+ IGHD6-13_star_01_20: 0.009738001391143055
105
+ IGHD6-13_star_01_3: 0.01947600278228611
106
+ IGHD6-13_star_01_4: 0.01947600278228611
107
+ IGHD6-13_star_01_5: 0.009738001391143055
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+ IGHD6-13_star_01_6: 0.009738001391143055
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+ IGHD6-13_star_01_7: 0.009738001391143055
110
+ IGHD6-13_star_01_8: 0.009738001391143055
111
+ IGHD6-13_star_01_9: 0.009738001391143055
112
+ insert_left_A: 0.15319134841509058
113
+ insert_left_C: 0.2757444271471631
114
+ insert_left_G: 0.18995727203471233
115
+ insert_left_T: 0.19608492597131594
116
+ - !!python/object:python.hmmwriter.State
117
+ emissions:
118
+ probs:
119
+ A: 0.04207395770235158
120
+ C: 0.04207395770235158
121
+ G: 0.8737781268929452
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+ T: 0.04207395770235158
123
+ track: nukes
124
+ extras:
125
+ ambiguous_char: N
126
+ ambiguous_emission_prob: 0.25
127
+ germline: G
128
+ name: insert_left_G
129
+ transitions:
130
+ IGHD6-13_star_01_0: 0.009738001391143055
131
+ IGHD6-13_star_01_1: 0.009738001391143055
132
+ IGHD6-13_star_01_10: 0.008656001236571604
133
+ IGHD6-13_star_01_11: 0.0075740010820001535
134
+ IGHD6-13_star_01_12: 0.006492000927428702
135
+ IGHD6-13_star_01_13: 0.005410000772857251
136
+ IGHD6-13_star_01_14: 0.0043280006182858
137
+ IGHD6-13_star_01_15: 0.0032460004637143497
138
+ IGHD6-13_star_01_16: 0.0021640003091428993
139
+ IGHD6-13_star_01_17: 0.001082000154571449
140
+ IGHD6-13_star_01_18: 0.009738001391143055
141
+ IGHD6-13_star_01_19: 0.009738001391143055
142
+ IGHD6-13_star_01_2: 0.009738001391143055
143
+ IGHD6-13_star_01_20: 0.009738001391143055
144
+ IGHD6-13_star_01_3: 0.01947600278228611
145
+ IGHD6-13_star_01_4: 0.01947600278228611
146
+ IGHD6-13_star_01_5: 0.009738001391143055
147
+ IGHD6-13_star_01_6: 0.009738001391143055
148
+ IGHD6-13_star_01_7: 0.009738001391143055
149
+ IGHD6-13_star_01_8: 0.009738001391143055
150
+ IGHD6-13_star_01_9: 0.009738001391143055
151
+ insert_left_A: 0.15319134841509058
152
+ insert_left_C: 0.2757444271471631
153
+ insert_left_G: 0.18995727203471233
154
+ insert_left_T: 0.19608492597131594
155
+ - !!python/object:python.hmmwriter.State
156
+ emissions:
157
+ probs:
158
+ A: 0.04207395770235158
159
+ C: 0.04207395770235158
160
+ G: 0.04207395770235158
161
+ T: 0.8737781268929452
162
+ track: nukes
163
+ extras:
164
+ ambiguous_char: N
165
+ ambiguous_emission_prob: 0.25
166
+ germline: T
167
+ name: insert_left_T
168
+ transitions:
169
+ IGHD6-13_star_01_0: 0.009738001391143055
170
+ IGHD6-13_star_01_1: 0.009738001391143055
171
+ IGHD6-13_star_01_10: 0.008656001236571604
172
+ IGHD6-13_star_01_11: 0.0075740010820001535
173
+ IGHD6-13_star_01_12: 0.006492000927428702
174
+ IGHD6-13_star_01_13: 0.005410000772857251
175
+ IGHD6-13_star_01_14: 0.0043280006182858
176
+ IGHD6-13_star_01_15: 0.0032460004637143497
177
+ IGHD6-13_star_01_16: 0.0021640003091428993
178
+ IGHD6-13_star_01_17: 0.001082000154571449
179
+ IGHD6-13_star_01_18: 0.009738001391143055
180
+ IGHD6-13_star_01_19: 0.009738001391143055
181
+ IGHD6-13_star_01_2: 0.009738001391143055
182
+ IGHD6-13_star_01_20: 0.009738001391143055
183
+ IGHD6-13_star_01_3: 0.01947600278228611
184
+ IGHD6-13_star_01_4: 0.01947600278228611
185
+ IGHD6-13_star_01_5: 0.009738001391143055
186
+ IGHD6-13_star_01_6: 0.009738001391143055
187
+ IGHD6-13_star_01_7: 0.009738001391143055
188
+ IGHD6-13_star_01_8: 0.009738001391143055
189
+ IGHD6-13_star_01_9: 0.009738001391143055
190
+ insert_left_A: 0.15319134841509058
191
+ insert_left_C: 0.2757444271471631
192
+ insert_left_G: 0.18995727203471233
193
+ insert_left_T: 0.19608492597131594
194
+ - !!python/object:python.hmmwriter.State
195
+ emissions:
196
+ probs:
197
+ A: 0.042073957702351575
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+ C: 0.042073957702351575
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+ G: 0.8737781268929452
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+ T: 0.042073957702351575
201
+ track: nukes
202
+ extras:
203
+ ambiguous_char: N
204
+ ambiguous_emission_prob: 0.25
205
+ germline: G
206
+ name: IGHD6-13_star_01_0
207
+ transitions:
208
+ IGHD6-13_star_01_1: 0.9615384615384616
209
+ end: 0.03846153846153846
210
+ - !!python/object:python.hmmwriter.State
211
+ emissions:
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215
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+ T: 0.04162444753266621
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+ track: nukes
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+ extras:
219
+ ambiguous_char: N
220
+ ambiguous_emission_prob: 0.25
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+ germline: G
222
+ name: IGHD6-13_star_01_1
223
+ transitions:
224
+ IGHD6-13_star_01_2: 0.9615384615384616
225
+ end: 0.03846153846153846
226
+ - !!python/object:python.hmmwriter.State
227
+ emissions:
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232
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+ track: nukes
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+ extras:
235
+ ambiguous_char: N
236
+ ambiguous_emission_prob: 0.25
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+ germline: G
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+ name: IGHD6-13_star_01_2
239
+ transitions:
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+ IGHD6-13_star_01_3: 0.9615384615384616
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+ end: 0.03846153846153846
242
+ - !!python/object:python.hmmwriter.State
243
+ emissions:
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+ extras:
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+ germline: T
254
+ name: IGHD6-13_star_01_3
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+ transitions:
256
+ IGHD6-13_star_01_4: 0.9615384615384616
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+ end: 0.03846153846153846
258
+ - !!python/object:python.hmmwriter.State
259
+ emissions:
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+ track: nukes
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+ extras:
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+ ambiguous_char: N
268
+ ambiguous_emission_prob: 0.25
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+ germline: A
270
+ name: IGHD6-13_star_01_4
271
+ transitions:
272
+ IGHD6-13_star_01_5: 0.9615384615384616
273
+ end: 0.03846153846153846
274
+ - !!python/object:python.hmmwriter.State
275
+ emissions:
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+ extras:
283
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284
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+ germline: T
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+ name: IGHD6-13_star_01_5
287
+ transitions:
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+ IGHD6-13_star_01_6: 0.9615384615384616
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+ end: 0.03846153846153846
290
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ ambiguous_emission_prob: 0.25
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+ germline: A
302
+ name: IGHD6-13_star_01_6
303
+ transitions:
304
+ IGHD6-13_star_01_7: 1.0
305
+ - !!python/object:python.hmmwriter.State
306
+ emissions:
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+ track: nukes
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315
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+ germline: G
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+ name: IGHD6-13_star_01_7
318
+ transitions:
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+ IGHD6-13_star_01_8: 0.989010989010989
320
+ end: 0.010989010989011004
321
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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329
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331
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+ germline: C
333
+ name: IGHD6-13_star_01_8
334
+ transitions:
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+ IGHD6-13_star_01_9: 0.978021978021978
336
+ end: 0.02197802197802199
337
+ - !!python/object:python.hmmwriter.State
338
+ emissions:
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347
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+ name: IGHD6-13_star_01_9
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+ end: 0.032967032967032975
353
+ - !!python/object:python.hmmwriter.State
354
+ emissions:
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+ germline: G
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+ end: 0.043956043956043966
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+ - !!python/object:python.hmmwriter.State
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+ end: 0.054945054945054944
385
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ end: 0.06593406593406594
401
+ - !!python/object:python.hmmwriter.State
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+ emissions:
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+ G: 0.8163951393095434
407
+ T: 0.045901215172614154
408
+ track: nukes
409
+ extras:
410
+ ambiguous_char: N
411
+ ambiguous_emission_prob: 0.25
412
+ germline: G
413
+ name: IGHD6-13_star_01_13
414
+ transitions:
415
+ IGHD6-13_star_01_14: 0.9230769230769231
416
+ end: 0.07692307692307691
417
+ - !!python/object:python.hmmwriter.State
418
+ emissions:
419
+ probs:
420
+ A: 0.03779855045065052
421
+ C: 0.8866043486480484
422
+ G: 0.03779855045065052
423
+ T: 0.03779855045065052
424
+ track: nukes
425
+ extras:
426
+ ambiguous_char: N
427
+ ambiguous_emission_prob: 0.25
428
+ germline: C
429
+ name: IGHD6-13_star_01_14
430
+ transitions:
431
+ IGHD6-13_star_01_15: 0.8846153846153846
432
+ end: 0.11538461538461536
433
+ - !!python/object:python.hmmwriter.State
434
+ emissions:
435
+ probs:
436
+ A: 0.04184768490474884
437
+ C: 0.04184768490474884
438
+ G: 0.04184768490474884
439
+ T: 0.8744569452857535
440
+ track: nukes
441
+ extras:
442
+ ambiguous_char: N
443
+ ambiguous_emission_prob: 0.25
444
+ germline: T
445
+ name: IGHD6-13_star_01_15
446
+ transitions:
447
+ IGHD6-13_star_01_16: 0.9102564102564102
448
+ end: 0.08974358974358974
449
+ - !!python/object:python.hmmwriter.State
450
+ emissions:
451
+ probs:
452
+ A: 0.04045667141156569
453
+ C: 0.04045667141156569
454
+ G: 0.8786299857653029
455
+ T: 0.04045667141156569
456
+ track: nukes
457
+ extras:
458
+ ambiguous_char: N
459
+ ambiguous_emission_prob: 0.25
460
+ germline: G
461
+ name: IGHD6-13_star_01_16
462
+ transitions:
463
+ IGHD6-13_star_01_17: 0.9358974358974359
464
+ end: 0.0641025641025641
465
+ - !!python/object:python.hmmwriter.State
466
+ emissions:
467
+ probs:
468
+ A: 0.04193819402378993
469
+ C: 0.04193819402378993
470
+ G: 0.8741854179286301
471
+ T: 0.04193819402378993
472
+ track: nukes
473
+ extras:
474
+ ambiguous_char: N
475
+ ambiguous_emission_prob: 0.25
476
+ germline: G
477
+ name: IGHD6-13_star_01_17
478
+ transitions:
479
+ IGHD6-13_star_01_18: 0.9615384615384616
480
+ end: 0.03846153846153846
481
+ - !!python/object:python.hmmwriter.State
482
+ emissions:
483
+ probs:
484
+ A: 0.04235381895368085
485
+ C: 0.04235381895368085
486
+ G: 0.04235381895368085
487
+ T: 0.8729385431389575
488
+ track: nukes
489
+ extras:
490
+ ambiguous_char: N
491
+ ambiguous_emission_prob: 0.25
492
+ germline: T
493
+ name: IGHD6-13_star_01_18
494
+ transitions:
495
+ IGHD6-13_star_01_19: 0.9615384615384616
496
+ end: 0.03846153846153846
497
+ - !!python/object:python.hmmwriter.State
498
+ emissions:
499
+ probs:
500
+ A: 0.8728027794603958
501
+ C: 0.04239907351320141
502
+ G: 0.04239907351320141
503
+ T: 0.04239907351320141
504
+ track: nukes
505
+ extras:
506
+ ambiguous_char: N
507
+ ambiguous_emission_prob: 0.25
508
+ germline: A
509
+ name: IGHD6-13_star_01_19
510
+ transitions:
511
+ IGHD6-13_star_01_20: 0.9615384615384616
512
+ end: 0.03846153846153846
513
+ - !!python/object:python.hmmwriter.State
514
+ emissions:
515
+ probs:
516
+ A: 0.042073957702351575
517
+ C: 0.8737781268929452
518
+ G: 0.042073957702351575
519
+ T: 0.042073957702351575
520
+ track: nukes
521
+ extras:
522
+ ambiguous_char: N
523
+ ambiguous_emission_prob: 0.25
524
+ germline: C
525
+ name: IGHD6-13_star_01_20
526
+ transitions:
527
+ end: 1.0
528
+ tracks:
529
+ nukes:
530
+ - A
531
+ - C
532
+ - G
533
+ - T